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Open Access Research article

Comparative physical maps derived from BAC end sequences of tilapia (Oreochromis niloticus)

Lucile Soler1, Matthew A Conte2, Takayuki Katagiri3, Aimee E Howe2, Bo-Young Lee2, Chris Amemiya4, Andrew Stuart4, Carole Dossat5, Julie Poulain5, Jeremy Johnson6, Federica Di Palma6, Kerstin Lindblad-Toh6, Jean-Francois Baroiller1, Helena D'Cotta1, Catherine Ozouf-Costaz7 and Thomas D Kocher2*

Author Affiliations

1 CIRAD-PERSYST, Aquaculture Research Unit, TA B-20/A, Campus International de Baillarguet, 34398 Montpellier cedex 5, France

2 Department of Biology, University of Maryland, College Park, Maryland 20742, USA

3 Laboratory of Fish Health Management, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-Ku Tokyo, 108-8477, Japan

4 Genome Resource Center, Benaroya Research Institute at Virginia Mason, 1201 Ninth Avenue, Seattle, WA 98101 USA

5 CEA, DSV, Genoscope, 2 rue Gaston Crémieux, CP5706 91057 Evry cedex, France

6 Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA

7 CNRS UMR 7138 « Systématique, Evolution, Adaptation », MNHN Département Systématique et Evolution, C.P. 26, 57 rue Cuvier 75231 PARIS Cedex 05, France

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BMC Genomics 2010, 11:636  doi:10.1186/1471-2164-11-636

Published: 16 November 2010

Abstract

Background

The Nile tilapia is the second most important fish in aquaculture. It is an excellent laboratory model, and is closely related to the African lake cichlids famous for their rapid rates of speciation. A suite of genomic resources has been developed for this species, including genetic maps and ESTs. Here we analyze BAC end-sequences to develop comparative physical maps, and estimate the number of genome rearrangements, between tilapia and other model fish species.

Results

We obtained sequence from one or both ends of 106,259 tilapia BACs. BLAST analysis against the genome assemblies of stickleback, medaka and pufferfish allowed identification of homologies for approximately 25,000 BACs for each species. We calculate that rearrangement breakpoints between tilapia and these species occur about every 3 Mb across the genome. Analysis of 35,000 clones previously assembled into contigs by restriction fingerprints allowed identification of longer-range syntenies.

Conclusions

Our data suggest that chromosomal evolution in recent teleosts is dominated by alternate loss of gene duplicates, and by intra-chromosomal rearrangements (~one per million years). These physical maps are a useful resource for comparative positional cloning of traits in cichlid fishes. The paired BAC end sequences from these clones will be an important resource for scaffolding forthcoming shotgun sequence assemblies of the tilapia genome.